DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=7.764e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1712 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	1775263	2R_1775263_SNP [dm3] 2R_5887758_SNP [dm6]	G	A	1.965e^-7	0.368	INTERGENIC
3R	6966512	3R_6966512_SNP [dm3] 3R_11140790_SNP [dm6]	A	C	1.804e^-6	1	INTERGENIC
3L	13114743	3L_13114743_SNP [dm3] 3L_13121643_SNP [dm6]	T	G	2.484e^-6	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	7072551	3R_7072551_SNP [dm3] 3R_11246829_SNP [dm6]	C	A	3.958e^-6	1	UTR_3_PRIME CG5214 DOWNSTREAM CR43283
3R	3118876	3R_3118876_SNP [dm3] 3R_7293154_SNP [dm6]	T	C	4.483e^-6	1	INTRON rn
3R	6960557	3R_6960557_SNP [dm3] 3R_11134835_SNP [dm6]	T	A	4.851e^-6	1	INTERGENIC
3R	14284865	3R_14284865_SNP [dm3] 3R_18459143_SNP [dm6]	G	T	5.085e^-6	1	INTRON fru	TF binding site mE1_TFBS_inv
3R	6960554	3R_6960554_SNP [dm3] 3R_11134832_SNP [dm6]	C	T	5.390e^-6	1	INTERGENIC
3L	10940355	3L_10940355_SNP [dm3] 3L_10947255_SNP [dm6]	C	T	6.088e^-6	1	INTERGENIC	TF binding site mE1_TFBS_inv
2L	10208145	2L_10208145_SNP [dm3] 2L_10208145_SNP [dm6]	G	A	7.826e^-6	1	SYNONYMOUS_CODING CG5731 UPSTREAM CR44845	TF binding site BDTNP1_TFBS_dl
X	12168506	X_12168506_SNP [dm3] X_12274473_SNP [dm6]	G	A	9.408e^-6	1	UPSTREAM CG45603 INTRON Ten-a
3R	3185877	3R_3185877_SNP [dm3] 3R_7360155_SNP [dm6]	C	A	1.047e^-5	1	INTERGENIC	insulator Insulator_Class_II.mE01
3R	9967112	3R_9967112_SNP [dm3] 3R_14141390_SNP [dm6]	G	T	1.186e^-5	1	INTERGENIC
3R	7121924	3R_7121924_SNP [dm3] 3R_11296202_SNP [dm6]	A	G	1.215e^-5	1	INTRON CR31386	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	2552127	3L_2552127_SNP [dm3] 3L_2552127_SNP [dm6]	A	C	1.228e^-5	1	INTRON Spn
3R	7122348	3R_7122348_SNP [dm3] 3R_11296626_SNP [dm6]	C	T	1.290e^-5	1	INTRON CR31386	TF binding site mE1_TFBS_chinmo
3R	14284870	3R_14284870_SNP [dm3] 3R_18459148_SNP [dm6]	G	A	1.392e^-5	1	INTRON fru	TF binding site mE1_TFBS_inv
3R	3023395	3R_3023395_SNP [dm3] 3R_7197673_SNP [dm6]	A	G	1.412e^-5	1	INTRON lap	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	3197386	3R_3197386_SNP [dm3] 3R_7371664_SNP [dm6]	A	C	1.437e^-5	1	INTERGENIC
2L	1390018	2L_1390018_SNP [dm3] 2L_1390018_SNP [dm6]	G	T	1.498e^-5	1	INTRON lea	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	6987046	3R_6987046_DEL [dm3] 3R_11161324_DEL [dm6]	AGCCAA	A	1.617e^-5	1	FRAME_SHIFT CG4757
X	12169461	X_12169461_SNP [dm3] X_12275428_SNP [dm6]	T	C	1.622e^-5	1	DOWNSTREAM CG45603 INTRON Ten-a
X	15612111	X_15612111_SNP [dm3] X_15718078_SNP [dm6]	G	C	1.664e^-5	1	SYNONYMOUS_CODING CG8184	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2R	12018954	2R_12018954_SNP [dm3] 2R_16131449_SNP [dm6]	G	A	1.747e^-5	1	INTRON spin	TF binding site mE1_TFBS_cad
3L	18832515	3L_18832515_SNP [dm3] 3L_18839415_SNP [dm6]	A	T	1.750e^-5	1	INTRON Indy	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	19477291	2R_19477291_SNP [dm3] 2R_23589768_SNP [dm6]	A	G	1.761e^-5	1	INTRON apt
2L	11351871	2L_11351871_SNP [dm3] 2L_11351871_SNP [dm6]	A	T	1.926e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
2L	7396526	2L_7396526_SNP [dm3] 2L_7396526_SNP [dm6]	C	T	1.929e^-5	1	UPSTREAM CG5160 INTRON CG5160
X	11003705	X_11003705_DEL [dm3] X_11109672_DEL [dm6]	TT	T	1.944e^-5	1	UPSTREAM Hsp60 INTRON Hsp60	TF binding site BDTNP1_TFBS_sna
3R	7395728	3R_7395728_SNP [dm3] 3R_11570006_SNP [dm6]	A	G	2.002e^-5	1	INTRON Mrp4	TF binding site mE1_TFBS_Trl
2R	20629833	2R_20629833_SNP [dm3] 2R_24742310_SNP [dm6]	T	C	2.041e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	2551767	3L_2551767_SNP [dm3] 3L_2551767_SNP [dm6]	C	A	2.220e^-5	1	INTRON Spn
3L	3001913	3L_3001913_SNP [dm3] 3L_3001913_SNP [dm6]	T	C	2.233e^-5	1	UTR_5_PRIME FMRFaR UPSTREAM FMRFaR
X	15603751	X_15603751_SNP [dm3] X_15709718_SNP [dm6]	C	T	2.291e^-5	1	UPSTREAM CG9281 & 1 other INTRON CG9281	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	6985311	3R_6985311_SNP [dm3] 3R_11159589_SNP [dm6]	G	T	2.308e^-5	1	UTR_3_PRIME Ugt86Da
3L	4969604	3L_4969604_SNP [dm3] 3L_4969604_SNP [dm6]	T	A	2.437e^-5	1	INTRON Con	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	13784725	2R_13784725_SNP [dm3] 2R_17897220_SNP [dm6]	T	A	2.477e^-5	1	INTRON Elk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2280167	2L_2280167_SNP [dm3] 2L_2280167_SNP [dm6]	G	A	2.488e^-5	1	UPSTREAM CR43753 INTERGENIC
2R	8493524	2R_8493524_SNP [dm3] 2R_12606019_SNP [dm6]	G	A	2.628e^-5	1	INTRON Amph
2R	20173752	2R_20173752_SNP [dm3] 2R_24286229_SNP [dm6]	G	A	2.714e^-5	1	INTRON nvy	TF binding site mE1_TFBS_chinmo
X	12174953	X_12174953_SNP [dm3] X_12280920_SNP [dm6]	C	G	2.740e^-5	1	INTRON Ten-a
2R	14395246	2R_14395246_DEL [dm3] 2R_18507741_DEL [dm6]	CTGTAACTGC	C	2.762e^-5	1	INTERGENIC
2R	1829387	2R_1829387_SNP [dm3] 2R_5941882_SNP [dm6]	T	A	2.769e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	3133376	3R_3133376_SNP [dm3] 3R_7307654_SNP [dm6]	A	G	3.009e^-5	1	INTRON rn
3L	15935511	3L_15935511_SNP [dm3] 3L_15942411_SNP [dm6]	A	T	3.031e^-5	1	INTRON Pka-C3
2L	1390063	2L_1390063_SNP [dm3] 2L_1390063_SNP [dm6]	A	T	3.044e^-5	1	INTRON lea	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	9678459	3L_9678459_SNP [dm3] 3L_9685359_SNP [dm6]	A	C	3.073e^-5	1	SYNONYMOUS_CODING CG16719 INTRON CG6767	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	7354200	3R_7354200_SNP [dm3] 3R_11528478_SNP [dm6]	C	G	3.174e^-5	1	INTERGENIC
3R	6965208	3R_6965208_SNP [dm3] 3R_11139486_SNP [dm6]	C	T	3.316e^-5	1	SYNONYMOUS_CODING CG4706
3R	26678424	3R_26678424_SNP [dm3] 3R_30852702_SNP [dm6]	T	G	3.445e^-5	1	INTRON tll	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	2551765	3L_2551765_SNP [dm3] 3L_2551765_SNP [dm6]	G	C	3.593e^-5	1	INTRON Spn
2L	22958110	2L_22958110_SNP [dm3] 2L_23065378_SNP [dm6]	C	T	3.685e^-5	1	INTERGENIC
3R	9049468	3R_9049468_SNP [dm3] 3R_13223746_SNP [dm6]	T	C	3.752e^-5	1	DOWNSTREAM Ace INTRON Ace
3L	2739280	3L_2739280_SNP [dm3] 3L_2739280_SNP [dm6]	T	A	3.908e^-5	1	UPSTREAM Acp62F INTRON Mrtf
3L	5385761	3L_5385761_SNP [dm3] 3L_5392661_SNP [dm6]	C	T	3.916e^-5	1	INTERGENIC
3L	4387501	3L_4387501_INS [dm3] 3L_4387501_INS [dm6]	C	TG	4.036e^-5	1	INTRON slow
3R	6965163	3R_6965163_SNP [dm3] 3R_11139441_SNP [dm6]	G	A	4.036e^-5	1	SYNONYMOUS_CODING CG4706
3R	6966359	3R_6966359_SNP [dm3] 3R_11140637_SNP [dm6]	C	A	4.082e^-5	1	DOWNSTREAM CG4706 INTERGENIC
2L	11351865	2L_11351865_SNP [dm3] 2L_11351865_SNP [dm6]	G	T	4.166e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3L	3563384	3L_3563384_SNP [dm3] 3L_3563384_SNP [dm6]	C	G	4.187e^-5	1	INTRON Eip63E
3R	14996543	3R_14996543_SNP [dm3] 3R_19170821_SNP [dm6]	T	C	4.380e^-5	1	DOWNSTREAM sqz INTERGENIC
3L	1012173	3L_1012173_INS [dm3] 3L_1012173_INS [dm6]	G	GG	4.388e^-5	1	INTRON trio
2L	10973758	2L_10973758_SNP [dm3] 2L_10973758_SNP [dm6]	G	A	4.403e^-5	1	SYNONYMOUS_CODING abo DOWNSTREAM CG16743
2L	22910462	2L_22910462_INS [dm3] 2L_23017730_INS [dm6]	T	TTTAGAATAT	4.408e^-5	1	INTRON Cht3
3L	2739349	3L_2739349_SNP [dm3] 3L_2739349_SNP [dm6]	C	T	4.576e^-5	1	UPSTREAM Acp62F INTRON Mrtf
3R	16774047	3R_16774047_SNP [dm3] 3R_20948325_SNP [dm6]	T	G	4.671e^-5	1	UPSTREAM Atpalpha INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
X	475482	X_475482_SNP [dm3] X_581449_SNP [dm6]	G	A	4.696e^-5	1	UPSTREAM vnd INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	12250640	3R_12250640_SNP [dm3] 3R_16424918_SNP [dm6]	C	A	4.893e^-5	1	DOWNSTREAM tRNA:CR31497 INTERGENIC	regulatory region REDfly_CRMs
3R	6456911	3R_6456911_SNP [dm3] 3R_10631189_SNP [dm6]	G	A	4.896e^-5	1	INTRON hth	TF binding site mE1_TFBS_cad
3R	3218622	3R_3218622_SNP [dm3] 3R_7392900_SNP [dm6]	G	C	4.952e^-5	1	DOWNSTREAM CG42650 INTERGENIC	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	14580173	2L_14580173_SNP [dm3] 2L_14580173_SNP [dm6]	A	G	4.972e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3R	6994931	3R_6994931_SNP [dm3] 3R_11169209_SNP [dm6]	A	C	5.106e^-5	1	NON_SYNONYMOUS_CODING Ugt35b	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	15603443	X_15603443_SNP [dm3] X_15709410_SNP [dm6]	A	C	5.210e^-5	1	UPSTREAM CG9281 INTRON CG9281	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2L	22936428	2L_22936428_SNP [dm3] 2L_23043696_SNP [dm6]	G	A	5.327e^-5	1	INTERGENIC
3R	7395598	3R_7395598_SNP [dm3] 3R_11569876_SNP [dm6]	A	C	5.400e^-5	1	INTRON Mrp4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	12819384	2R_12819384_SNP [dm3] 2R_16931879_SNP [dm6]	A	G	5.432e^-5	1	INTRON Pkc53E
2L	22975447	2L_22975447_SNP [dm3] 2L_23082715_SNP [dm6]	C	T	5.462e^-5	1	INTERGENIC
3R	9783523	3R_9783523_SNP [dm3] 3R_13957801_SNP [dm6]	C	T	5.483e^-5	1	UPSTREAM Ipp INTERGENIC
X	16621037	X_16621037_SNP [dm3] X_16727004_SNP [dm6]	A	G	5.508e^-5	1	DOWNSTREAM CG9634 & 1 other INTERGENIC
2R	8268804	2R_8268804_SNP [dm3] 2R_12381299_SNP [dm6]	A	G	5.522e^-5	1	UPSTREAM CG13155 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	15603248	X_15603248_SNP [dm3] X_15709215_SNP [dm6]	G	T	5.570e^-5	1	UPSTREAM CG9281 INTRON CG9281	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	15603532	X_15603532_DEL [dm3] X_15709499_DEL [dm6]	TT	T	5.581e^-5	1	UPSTREAM CG9281 INTRON CG9281	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
3L	9502956	3L_9502956_SNP [dm3] 3L_9509856_SNP [dm6]	T	A	5.607e^-5	1	UTR_3_PRIME RpS9 UPSTREAM CG3408 DOWNSTREAM RpS9 & 1 other	TF binding site BDTNP1_TFBS_dl
3L	10898012	3L_10898012_SNP [dm3] 3L_10904912_SNP [dm6]	G	A	5.722e^-5	1	INTERGENIC
3L	10570990	3L_10570990_SNP [dm3] 3L_10577890_SNP [dm6]	A	C	5.843e^-5	1	INTRON A2bp1
3L	16379635	3L_16379635_DEL [dm3] 3L_16386535_DEL [dm6]	AT	C	6.215e^-5	1	UTR_5_PRIME RAF2 UPSTREAM CG4729 INTRON RAF2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
2L	7397098	2L_7397098_SNP [dm3] 2L_7397098_SNP [dm6]	C	A	6.380e^-5	1	INTRON CG5160
3L	2552346	3L_2552346_SNP [dm3] 3L_2552346_SNP [dm6]	G	C	6.381e^-5	1	INTRON Spn	TF binding site BDTNP1_TFBS_dl
3R	25675409	3R_25675409_SNP [dm3] 3R_29849687_SNP [dm6]	T	C	6.450e^-5	1	SYNONYMOUS_CODING Cad99C	TF binding site mE1_TFBS_cad
3L	1671813	3L_1671813_SNP [dm3] 3L_1671813_SNP [dm6]	G	T	6.618e^-5	1	SYNONYMOUS_CODING CG13930	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10940643	3L_10940643_DEL [dm3] 3L_10947543_DEL [dm6]	TCTGGA	T	6.631e^-5	1	INTERGENIC
3L	10940642	3L_10940642_SNP [dm3] 3L_10947542_SNP [dm6]	T	G	6.658e^-5	1	INTERGENIC
3R	11255602	3R_11255602_SNP [dm3] 3R_15429880_SNP [dm6]	A	G	6.678e^-5	1	INTRON CG6118
3L	10940631	3L_10940631_DEL [dm3] 3L_10947531_DEL [dm6]	AAATACTAG	A	6.686e^-5	1	INTERGENIC
3R	23293307	3R_23293307_MNP [dm3] 3R_27467585_MNP [dm6]	GGC	ACT	6.699e^-5	1	DOWNSTREAM CG13978 INTERGENIC	TF binding site mE1_TFBS_inv
3R	23293269	3R_23293269_INS [dm3] 3R_27467547_INS [dm6]	T	TCGGCGGACTGAT...	6.743e^-5	1	DOWNSTREAM CG13978 INTERGENIC	TF binding site mE1_TFBS_inv
2R	20294488	2R_20294488_SNP [dm3] 2R_24406965_SNP [dm6]	G	A	6.869e^-5	1	SYNONYMOUS_CODING SerT	TF binding site mE1_TFBS_chinmo
2R	15532707	2R_15532707_SNP [dm3] 2R_19645202_SNP [dm6]	A	T	6.870e^-5	1	INTERGENIC
2L	22912783	2L_22912783_SNP [dm3] 2L_23020051_SNP [dm6]	A	G	6.919e^-5	1	INTRON Cht3
2R	17812675	2R_17812675_SNP [dm3] 2R_21925170_SNP [dm6]	C	T	6.939e^-5	1	INTRON Fili

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By genomic position
Variant impact
Gene name

mn_Glucose_LowDiet phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results